jbedo Justin Bedő
github.com/jbedo · maintains 34 packages (34 directly), sole maintainer of 27, member of 0 teams
34 packages
| Package ▲ | Version | Maintainers | # | Teams | Deps | Used by | Used by (transitive) | Status |
|---|---|---|---|---|---|---|---|---|
Free software environment for statistical computing and graphics |
4.6.1 |
3 | 31 | 36 | 52 | maintained | ||
Application containers for linux (previously known as Singularity) |
1.5.4 |
2 | 21 | 0 | 0 | maintained | ||
1.5.4 |
2 | 21 | 0 | 0 | maintained | |||
Suite of tools for addressing questions arising in genomics studies |
2.4.42 |
1 | 6 | 0 | 0 | single | ||
Powerful toolset for genome arithmetic |
2.31.1 |
1 | 7 | 2 | 2 | single | ||
Ultra-fast all-in-one FASTQ preprocessor |
1.4.0 |
1 | 7 | 0 | 0 | single | ||
Ultra-fast computation of genome mappability |
1.3.0 |
1 | 5 | 0 | 0 | single | ||
Graph based aligner |
2.2.3 |
1 | 6 | 0 | 0 | single | ||
Collection of optimised low-level functions targeting storage applications |
2.32.1 |
1 | 6 | 7 | 8,436 | single | ||
Genomic sequence aligner |
1654 |
1 | 6 | 1 | 1 | single | ||
Short read genome assembler |
3.2.1 → 3.2.6 |
1 | 5 | 1 | 1 | single outdated | ||
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing |
0.3.14 |
1 | 6 | 0 | 0 | single | ||
Bayesian haplotype-based mutation calling |
0.7.4 |
1 | 9 | 0 | 0 | single | ||
Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF |
3.5.0 |
1 | 4 | 0 | 0 | single | ||
Tools for manipulating biological data, particularly multiple sequence alignments |
0.14.0 → 0.15.1 |
1 | 21 | 0 | 0 | single outdated | ||
Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data |
0.9.13 → 0.9.14 |
1 | 30 | 0 | 0 | single outdated | ||
Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index |
0.9.0.4 |
1 | 19 | 1 | 1 | single | ||
Python bindings for the LZO data compression library |
1.16 |
1 | 19 | 1 | 1 | single | ||
Tools for manipulating biological data, particularly multiple sequence alignments |
0.14.0 → 0.15.1 |
1 | 21 | 1 | 1 | single outdated | ||
Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data |
0.9.13 → 0.9.14 |
1 | 30 | 0 | 0 | single outdated | ||
Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index |
0.9.0.4 |
1 | 19 | 1 | 1 | single | ||
Python bindings for the LZO data compression library |
1.16 |
1 | 19 | 5 | 6 | single | ||
Free software environment for statistical computing and graphics |
4.6.1-wrapper |
3 | 5 | 0 | 0 | maintained | ||
SAM/BAM processing tool |
1.0.1 |
1 | 7 | 0 | 0 | single | ||
Tool for marking duplicates and extracting discordant/split reads from SAM/BAM files |
0.1.26 |
1 | 2 | 0 | 0 | single | ||
Application containers for linux (Sylabs Inc's fork of Singularity, a.k.a. SingularityCE) |
4.4.1 → 4.5.1 |
2 | 22 | 1 | 1 | maintained outdated | ||
4.4.1 → 4.5.1 |
2 | 22 | 0 | 0 | maintained outdated | |||
Genetic variant annotation and effect prediction toolbox |
4.3t → 5.4c |
1 | 5 | 0 | 0 | single outdated | ||
C++ SQLite3 wrapper |
3.4.0 |
2 | 5 | 0 | 0 | maintained | ||
Read aligner for short reads |
0.17.0 |
1 | 6 | 0 | 0 | single | ||
High-performance read alignment, quantification and mutation discovery |
2.1.1 |
1 | 3 | 0 | 0 | single | ||
Find and characterise transposable element insertions |
1.1 |
1 | 24 | 0 | 0 | single broken | ||
Variant calling and somatic mutation/CNV detection for next-generation sequencing data |
2.4.6 |
1 | 4 | 0 | 0 | single unfree | ||
Utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins |
1.0.2 |
1 | 16 | 0 | 0 | single |